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We are proud to announce that Protocol Online has just launched its first scientific journal – Journal of Biological Methods(JBM, ISSN 2326-9901)!

Since its launch in 1999, Protocol Online has received hundreds of submissions of methods and protocols from worldwide researchers. To meet the growing needs of our contributors and provide them with formal publishing opportunities, Protocol Online created this new multidisciplinary and open-access journal.

JBM is committed to publishing high quality peer-reviewed papers on cutting-edge and innovative biological techniques, methods and protocols.

The editors of JBM invite submission of papers for its inaugural issue to be published in October 2013. Manuscripts submitted for consideration are expected to describe original research on novel biotechnology, biological methods and experimental techniques, significant optimization and modification of existing methods, development of step-by-step protocols based on proven methods and technologies, and reviews on technical aspects of a particular biological field. JBM covers all biological sciences including, but not limited to, the following areas: Biochemistry, Bioinformatics, Biomedical science, Biotechnology, Cancer biology, Cell biology, Chemical biology, Epigenetics, Genetics and genomics, Immunology, Microbiology, Model organisms, Molecular biology, Nanotechnology, Neuroscience, Physiology, Plant biology, Signal transduction, Stem cells, and Zoology.

Types of articles include Research Articles, Protocols, Reviews, and Application Notes.

JBM is also inviting applications for positions on its Editorial Board. Please see the announcement on JBM website for details. Qualified individuals should send their applications to the editor at "editor at jbmethods.org".

Hey guys,
Being a relatively new graduate student in a big lab where people do not have time to train me, I wanted to train myself. I read this book "At the bench" by Kathy Barker and wrote down things which were important for me. But nevertheless I thought it might be useful to somebody else also. I've attached the document with this post.
Enjoy!

Attached Files

1. He had only one major publication.
2. It was in Hebrew.
3. It had no references.
4. It wasn't even published in a refereed journal.
5. Some even doubt he wrote it himself.
6. It may be true that he created the world, but what has he done since then?
7. His cooperative efforts have been quite limited.
8. The scientific community has had a hard time replicating his results.
9. He never applied to the Ethics Board for permission to use human subjects.
10. When one experiment went awry he tried to cover it up by drowning the subjects.
11. When subjects didn't behave as predicted, he deleted them from the sample.
12. He rarely came to class, just told students to read the Book.
13. Some say he had his son teach the class.
14. He expelled his first two students for learning.
15. Although there were only ten requirements, most students failed his tests.
16. His office hours were infrequent and usually held on a mountaintop.

Many people have problem identifying or predicting the promoter sequence of a gene, or don't know how to get the actual sequence for analysis such as primer design, transcription factor binding site search, etc. Here I provide ways how I do these things.

1. How to find and retrieve promoter sequences from genome databases

Promoter sequences are usually the sequence immediately upstream the transcription start site (TSS) or first exon. If we know the TSS of a gene, we will know with confidence where the promoter is even without experimental characterization. For many organisms, such as as human, mouse, the genome is well annotated and TSS well defined. Thus promoter sequence retrieval is an easy task. There are three major genome browsers: NCBI, Ensembl and UCSC. For our purpose, Ensembl provides the most convenient interface. Here is an example:

On the left, under "Gene Summary", click "Sequence", the sequence of the gene including 5' flanking, exons, introns and flanking region will be displayed.

The exons are high lighted in pink background and red text, the sequence in front of the first exon is the promoter sequence.

By default, 600 bp 5'-flanking sequence (promoter) is displayed. If you want to get more, click "Configure this page" in the lower left column, a popup window opens allowing to input the size of 5' Flanking sequence (upstream). You can put for example "1000" and then save the configuration.

Sometimes there are discrepancies between Ensembl and UCSC annotation regarding TSS. To make sure the first exon given by ensembl is right, copy the promoter sequence

Go to UCSC BLAT search at http://genome.ucsc.e...t?command=start and choose the right genome (eg, human), paste the sequence there. On the result page, click browse of the first hit, this will bring you to the genome browser Page. the query sequence is now aligned with UCSC genome sequence. Zoom out a bit, you will be able to determine whether the promoter sequence matches UCSC annotation. If it matches, the sequence is very likely the right one. Here is the BRCA2 promoter sequence aligned to BRAC2 gene.

In UCSC genome broswer, you can turn on CpG island feature, if there is CpG island in the promoter sequence, the sequence is highly likely a true promoter. In the above example (BRCA2), a CpG island is displayed in the proximal promoter.

Beware some genes have alternative promoters. To find those sequences, it requires extensive bioinformatics and experimental analysis.